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A PCA-based method for ancestral informative markers selection in structured populations

Science china(Life Sciences) 2009年第10期52卷 972-976页

作者： ZHANG Feng1,3, ZHANG Lei1,3 & DENG Hong-Wen1,2,3 1 Key Laboratory of Biomedical Information Engineering of Ministry of Education, Institute of Molecular Genetics, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, china 2 Institute of Bioscience and biotechnology, School of Science, beijing Jiaotong University, beijing 100044, china 3 Departments of Orthopedic Surgery and Basic Medical Science, School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA Key Laboratory of Biomedical Information Engineering of Ministry of Education Institute of Molecular Genetics School of Life Science and Technology Xi'an Jiaotong University Xi'an 710049 China.

Identification of population structure can help trace population histories and identify disease genes. Structured association (SA) is a commonly used approach for population structure identification and association mapping. A major issue with SA is that its performance greatly depends on the informa-tiveness and the numbers of ancestral informative markers (AIMs). Present major AIM selection meth-ods mostly require prior individual ancestry information, which is usually not available or uncertain in practice. To address this potential weakness, we herein develop a novel approach for AIM selection based on principle component analysis (PCA), which does not require prior ancestry information of study subjects. Our simulation and real genetic data analysis results suggest that, with equivalent AIMs, PCA-based selected AIMs can significantly increase the accuracy of inferred individual ancestries compared with traditionally randomly selected AIMs. Our method can easily be applied to whole genome data to select a set of highly informative AIMs in population structure, which can then be used to identify potential population structure and correct possible statistical biases caused by population stratification.

关键词： population structure principle component analysis ancestral informative markers

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Cloning and characterization of cotton heteromeric acetyl-CoA carboxylase genes

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Progress in Natural Science:Materials International 2007年第12期17卷 1412-1418页

作者： Qiao Zhixin and Liu Jinyuan(Laboratory of Molecular Biology and Protein Science Laboratory of the Ministry of Education, Department of Biological Sciences and biotechnology, Tsinghua University, beijing 100084, china) Laboratory of Molecular Biology and Protein Science Department of Biological Sciences and Biotechnology Tsinghua University Beijing 100084 China

Heteromeric acetyl-coenzyme A (CoA) carboxylase (ACCase) catalyzes the formation of malonyl-CoA from acetyl-CoA. It plays an essential role in fatty acid synthesis in prokaryotes and most of plants. The heteromeric ACCase is composed of four subunits: biotin carboxylase (BC), biotin carboxyl carrier protein (BCCP), and α- and β-subunits of carboxyltransferase (α- and β-CT). In this study, we cloned five novel genes encoding the subunits of heteromeric ACCase (one BC, BCCP and β-CT, and two α-CTs) from cotton (Gossypium hirsutum cv. zhongmian 35) by RACE-PCR. The deduced amino acid sequence of these cDNAs shares high similarity with other reported heteromeric ACCase subunits. The phylogenetic analysis indicated that the different subunits of heteromeric ACCase were grouped in a similar pattern. Southern blot analysis revealed the milti-copy patterns of these heteromeric ACCase genes in cotton genome. Semi-quantitative RT-PCR demonstrated that heteromeric ACCase genes were constitutively expressed in all of the cotton tissues, but the transcripts accumulated at a relatively low level in roots. To our knowledge, this is the first report about characterization of the heteromeric ACCase genes in cotton.

关键词： heteromeric ACCase cotton gene cloning fatty acid synthesis.

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In vitro and in vivo evaluation of a novel oral insulin formulation

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Acta Pharmacologica Sinica 2006年第10期27卷 1382-1388页

作者： Er-li MA Hong MA Zheng LIU Chang-xue ZHENG Ming-xing DUAN~2 State Key Laboratory of Bio-membrane and biotechnology,Department of Biological Sciences and biotechnology,Tsinghua University beijing 100084,china Department of Biological Sciences and biotechnology State Key Laboratory of Bio-membrane and Biotechnology Tsinghua University Beijing China

Aim:To develop a stable self-emulsifying formulation for oral delivery of ***:Caco-2 cell line and diabetic beagles were used as in vitro and in vivomodels to study the absorption mechanism and the hypoglycemic efficacy of *** addition,various physicochemical parameters of the formulationsuch as droplet size,insulin encapsulation efficiency and stability were ***:This formulation enabled changes in barrier properties of Caco-2monolayers,as referred by transepithelial electrical resistance(TEER)and appar-ent permeability coefficients(Papp)of the paracellular marker ranitidine(20-foldgreater than control)but not transcellular marker propranolol,suggesting that theopening of tight junctions was *** diabetic beagle dogs,the bioavailabilityof this formulation was up to 15.2% at a dose of 2.5 IU/kg in comparison with thehypoglycemic effect of native insulin(0.5 IU/kg)delivered by ***:This formulation,recently approved by the china StateFood and Drug Administration to enter clinical trials,was stable,degradation-protected and absorption-enhanced,and provided a promising formulation fororal insulin delivery.

关键词： insulin oral delivery Caco-2 diabetic beagles

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Mitochondrial membrane fusion and ATP synthesis both compete for interfacial △pH of PMF,but not △Ψ:An Inter-play between membrane fusion and energy coupling of mitochondria

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生物物理学报 2009年第S1期25卷 217-218页

作者： Shusen Liu State Key Laboratory of Biomembrane and Membrane biotechnology, Instutute of Zoology, Chinese Academy of Sciences, beijing, 100101, china

Although some fusogenic proteins have been established to tether two opposite outer or inner mitochondrial membranes into contact, a prerequisite for whole mitochondrial fusion events,

关键词： Mitochondrial membrane fusion Protein-tethering Lipid-bilayer-mixing and fusion Interfacial △pH of PMF.Inter-play between membrane fusion and ATP synthesis.

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Molecular cloning and characterization of a cotton phosphoenolpyruvate carboxylase gene

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Progress in Natural Science:Materials International 2008年第5期18卷 539-545页

作者： Zhixin Qiao, Jin-Yuan Liu Laboratory of Molecular Biology and Protein Science Laboratory of the Ministry of Education, Department of Biological Sciences and biotechnology, Tsinghua University, beijing 100084, china Laboratory of Molecular Biology and Protein Science Laboratory of the Ministry of Education Department of Biological Sciences and Biotechnology Tsinghua University Beijing 100084 China

Phosphoenolpyruvate carboxylase (PEPC) plays diverse physiological functions during plant development. In this study, a new phos- phoenolpyruvate carboxylase gene GhPEPC2 is isolated from cotton (Gossypium hirsutum cv. zhongmian 35) by RACE-PCR. The cloned cDNA of GhPEPC2 is 3364 bp in length, and has an open reading frame of 2913 bp, encoding for 971 putative amino acids with a calculated molecular mass of 110.6 kD and pI of 5.56. The deduced amino acid sequence of GhPEPC2 shares high similarity with other reported plant PEPCs. Southern blot analysis indicates that the cotton PEPC exists as a small gene family and the GhPEPC2 might have two copies in the cotton genome. The semi-quantitative RT-PCR reveals that GhPEPC2 constitutively expresses in all the tissues of cot- ton and accumulated highly in roots, owers and embryos but relatively low in stems and bers. In addition, the recombinant GhPEPC2 has been puri ed by expressing it in Escherichia coli and the catalytic properties of it were also investigated. The results showed that GhPEPC2 is a typical C3 PEPC with a higher Km (83.6 lM) and lower Vmax (8.0 lmol min 1 mg 1) compared with the C3 PEPCs pre- viously reported.

关键词： Phosphoenolpyruvate carboxylase Recombinant protein Southern blot Cotton

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A multi-dimensional microcanonical Monte Carlo study of S_0→T_1 intersystem crossing of isocyanic acid

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Science china Chemistry 2009年第11期52卷 1885-1891页

作者： ZHANG Feng1,2,FANG WeiHai1,LUO Yi2 & LIU RuoZhuang1 1 College of Chemistry,beijing Normal University,beijing 100875,china 2 Theoretical Chemistry,School of biotechnology,Royal Institute of Technology,S-10691 Stockholm,Sweden College of Chemistry Beijing Normal University Beijing China Theoretical Chemistry School of Biotechnology Royal Institute of Technology Stockholm Sweden

A general formula for the multi-dimensional Monte Carlo microcanonical nonadiabatic rate constant expressed in configuration space is applied to calculate the rate of intersystem crossing(ISC) between the ground(S0) and first excited triplet(T1) states for isocyanic ***-,two-and three-dimensional potential energy surfaces are constructed by coupled-cluster single-double CCSD calculations,which are used for Monte Carlo *** calculated S0→T1 ISC rate is in good agreement with experimental findings,which gives us a reason to believe that the multi-dimensional Monte Carlo microcanonical nonadiabatic rate theory is a very effective method for calculating nonadiabatic transition rate of a polyatomic molecule.

关键词： multi-dimensional Monte Carlo microcanonical nonadiabatic rate theory intersystem crossing isocyanic acid nonadiabatic transition

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The Meiotic Behavior of an Alien Chromosome in Triticum aestivum-Haynaldia villosa Monosomic Addition Lines

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Agricultural Sciences in china 2002年第4期1卷 370-374页

作者： LI Rui-fen, LIANG Hong-xia and ZHAO Mao-lin(beijing Agricultural biotechnology Research Center , beijing Academy of Agricultural and Forestry Sciences , beijing 100089 , P.R. china) beijing Agricultural biotechnology Research Center Beijing Academy of Agricultural and Forestry Sciences Beijing 100089 P.R. China

By the combination of cytological analysis and using genomic in situ hybridization technique to identify an alien chromosome in wheat-Haynaldia villosa monosomic addition lines, we studied the meiotic behavior of the alien chromosome. The results indicated that the frequency of bivalent pairing was lower than the value expected in PMCs of two monosomic addition lines, the frequency of wheat chromosomes unpairing increased, and the wheat homologous chromosome pairing was interfered with by the added chromosome 6V at metaphase I. The chromosome 6V lagged in 20.3% -29.3% of PMCs, sister chromatids 6V early divided in 29.0% - 34.1% of PMCs, the single chromosome 6V in 18.2% - 26.1% of PMCs went to a pole randomly, the breakage frequency of chromosome 6V was 1.2% - 2.9%. Meanwhile, it was also found that several wheat chromosomes showed earlier division, lagging and breakage in a few PMCs. It revealed that the added chromosome 6V influenced the behavior of wheat chromosomes at anaphase. It was also found that the translo-cation was produced between 6V and wheat chromosomes in 1.2% of PMCs. It offered evidence for transloca-tion between wheat and Haynaldia villosa 6V chromosomes.

关键词： Wheat Haynaldia villosa Monosomic addition Meiosis GISH Translocation

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Thymic epithelial progenitor cells and thymus regeneration: an update

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Cell Research 2007年第1期17卷 50-55页

作者： L ianjun Zhang~(1,2) Liguang Sun~(1,3) Yong Zhao~1 ~1Transplantation Biology Research Division,State Key Laboratory of Biomembrane and Membrane biotechnology,Institute of Zoology,~2Graduate University of the Chinese Academy of Sciences,Chinese Academy of Sciences,beijing 100080,china,~3School of Public Health,Jilin University,Changchun 130021,china Transplantation Biology Research Division State Key Laboratory of Biomembrane and Membrane Biotechnology Institute of Zoology Chinese Academy of Sciences Beijing China Graduate University of the Chinese Academy of Sciences Chinese Academy of Sciences Beijing China School of Public Health Jilin University Changchun China

The thymus provides the essential microenvironment for T-cell development and *** epithelial cells(TECs),which are composed ofthymic cortical epithelial cells (cTECs) and thymic medullary epithelial cells (mTECs),have been well documented to be critical for these tightly regulated *** has long been controversial whether thecommon progenitor cells of TECs could give rise to both cTECs and *** progress has been made to charac-terize the common TEC progenitor cells in recent *** herein discuss the sole origin paradigm with regard to TECdifferentiation as well as these progenitor cells in thymus regeneration.

关键词： thymic epithelial progenitor cells thymus organogenesis thymus regeneration

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Effects of Aging and Advanced Glycation on Gene Expression in Cerebrum and Spleen of Mice

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Biomedical and Environmental Sciences 2003年第4期16卷 323-332页

作者： YUE-XIN LIANG, ZHEN WANG, DIAN-DONG LI, JIAN-MIN JIANG,AND RONG-GUANG SHAOInstitute of Medicinal biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, beijing 100050, china Institute of Medicinal biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College 北京 100050

Objective To analyze the effects of aging or advanced glycation on gene expression in the cerebrum and spleen of female C57BL/6J mice. Methods The gene expression profile was determined by using cDNA expression arrays containing 588 cDNA. Results Aging and advanced glycation resulted in differential gene expression patterns of cerebrum and spleen compared with young mice. Among the 80 genes detected in cerebrum, 43 exhibited a change in mRNA ratios with aging or treatment. Thirty-four changes (79%) were common in aged and D-galactose treated mice, whereas the cerebrum from aged and AGE-lysine treated mice showed common changes in expression of 38 genes (88%). Of the 86 genes detected in spleen, 29 (34%) displayed an age-related decrease in expression, whereas 3 (3%) displayed an increase in expression levels with aging. Eighteen genes from the detectable genes exhibited expression changes in both cerebrum and spleen of mice. Conclusions The gene expression profiles of D-galactose and AGE-lysine treated mice resemble those of aged mice. Use of cDNA hybridization arrays may provide a promising tool to explore the mechanism of aging at a molecular level.

关键词： Aging Galactose Advanced glycation Gene expression DNA microarrays Cerebrum Spleen

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Organic Solvents Mediate Self-assembly of GAV-9 Peptide on Mica Surface

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Acta Biochimica et Biophysica Sinica 2007年第4期39卷 285-289页

作者： Hai LI~(1,3) Feng ZHANG~1 Yi ZHANG~1* Jianhua HE~1 Jun HU~(1,2) 1 Shanghai Institute of Applied Physics,Chinese Academy of Sciences,Shanghai 201800,china 2 Bio-X Life Sciences Research Center.College of Life Science and biotechnology,Shanghai Jiaotong University,Shanghai 200030,china 3 Graduate School of the Chinese Academy of Sciences,beijing 100049,china Shanghai Institute of Applied Physics Chinese Academy of SciencesShanghai 201800 China Graduate School of the Chinese Academy of Sciencesbeijing 100049 China Bio-X Life Sciences Research Center College of Life Science and Biotechnology Shanghai Jiaotong UniversityShanghai 200030 China

Self-assembly of peptides into fibrils and other morphologies has attracted much attention inmany fields,especially in nanofabrication,pathology and *** this paper,self-assembly of GAV-9peptide in organic solvents,ethanol and acetone,was investigated using atomic force microscopy(AFM)and attenuated total reflectance-Fourier transform infrared spectroscopy(ATR-FTIR).The results indicatedthat GAV-9 self-assembled into various nanostructures in both solvents after deposited and evaporated *** with β-sheet conformation were observed in both solvents when the peptide concentrationwas higher than 280 μ***,ordered fibrils with β-sheet conformation were formed in ethanol,butnot in acetone,with a peptide concentration ranging from 7 μM to 28 μ*** attribute the formation ofvarious nanostructures to the different physicochemical properties of the polar organic solvents on the self-assembly of GAV-9 peptide.

关键词： self-assembly GAV-9 peptide organic solvents ATR-FTIR AFM

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